Soil aeration is considered the third most important factor affecting soil fertility (after water and nutrient availability). The main reasons for poor soil aeration are slow drainage, excessive precipitation or irrigation, or a sealing soil cover. Shallow groundwater impedes drainage by reducing the downwardly hydraulic gradient, which consequently increases the water content of the soil in the root zone, thus limiting soil aeration. In this study, we examined the effects of different parameters (e.g., soil texture, depth of groundwater table) on the severity of oxygen deficiency in the root zone of a mature Valencia orange (Citrus sinensis) grove planted above shallow groundwater. In addition, we examined the effect of the O2 stress level on tree growth, yield, and fruit quality. We also evaluated the effects of air injection and of irrigation intensity on tree growth, yield, fruit quality, and O2 concentration in the soil’s air, and looked into the (technical and economic) feasibility of air injection into the soil. We found that insufficient soil aeration significantly inhibited tree growth and reduced the yield. The soil texture (i.e., clay content) had a substantial effect on the yield, mainly because of its effect on the soil’s water retention. While soil O2 concentration slightly increased by air injection, the differences in tree growth, yield, and fruit quality parameters were not significant. The O2 concentration of the soil air alone was found to be a poor quantifier of soil aeration status. The Damkholer number (Da), evaluated from the measured soil O2 profiles and groundwater table depths is a superior quantifier for the prevailing aeration status. It can also be used for analyzing the effect of irrigation water quality on soil aeration status and respiration rates.